How to calculate allele frequencies from SNP's to determine LD

Question

[ojinjide]

I know this topic has been covered multiple times, but after reading the posts I am still having difficulty making my question fit. I have been given 2 SNPS: AAAAAAATATTT and CCCGGGCGGGGG respectively. Each genotype count is 250, 200, 40, 300, 120, and 90 respectively. I have been asked to calculate the allelic frequencies to determine LD and I am unable to. Any suggestions?

Answer 1

[mastal511]

See this web page for how to get allele freq from genotype freq.

https://www.ndsu.edu/pubweb/~mcclean/plsc431/popgen/popgen2.htm

Then see this wikipedia article for different measures of LD, and how to calculate them.

https://en.wikipedia.org/wiki/Linkage_disequilibrium

Answer 2

[ojinjide]

I am looking closely at the links now! Thank you for the direction.

Answer 3

[ojinjide]

I was able to easily calculate the frequencies. Thank you again!